Lili-Cao

random seed

9

### Issue summary Hi, I am wondering why the gnina results are different when I use the same parameters and run many replicas. I didn't set a value to the...

how to describe a terminal atom type with openff

7

**Describe the bug** **Output** **Computing environment (please complete the following information):** - Operating system - Output of running `conda list` **Additional context**

water

4

### Issue summary Hi, I am wondering if water molecules in a protein pdb file would be sampled during gnina docking process, with refinement used only in the rescore level...

different scores meaning

2

### Issue summary hi, Could you please explain what is the the meaning of the scores in the output? CNN_VS CNNaffinity CNN_score minimizedAffinity Thank you! ### Steps to reproduce ###...

OSError: torch_scatter/_version_cpu.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs

2

### 😵 Describe the installation problem I have pytorch 2.3.1 cpu_generic_py310ha4c588e_0 conda-forge installed and I want to use torchdrug. I have installed pip install torch_geometric pip install ninja wheel pip...

how to keep Hs after docking

6

### Issue summary Hi, I am wondering if it is possible to keep the protons of ligands after docking, is so, how should I do that? Thanks! Lili ### Steps...

empirical scoring functions used in each step

6

### Issue summary Hi May I ask what empirical scoring functions are used in the Monte Carlo chain, the refinement after the aggregating the top poses from each MC chain,...